单细胞marker基因平均表达量热图

最近有小伙伴问道如下的文献图，简单明了的一种细胞一列进行marker gene表达展示。这个图其实就是展示了平均的细胞表达量而已。我们简单做一下。此外，顺便复现下基因注释。

图片

（reference：Dissecting the transcriptome landscape of the human fetal neural retina and retinal pigment epithelium by single-cell RNA-seq analysis）首先我们得到marker gene：

library(Seurat)
human_data <- readRDS("D:/KS/human_data.rds")
DefaultAssay(human_data) <- "RNA"
all.markers  <- FindAllMarkers(human_data, 
                               only.pos = TRUE, 
                               min.pct = 0.25, 
                               logfc.threshold = 0.75)

选择需要的marker gene进行展示，平均表达量使用seurat自带函数AverageExpression进行计算。热图使用Complexheatmap做即可。

#计算平均表达量
gene_cell_exp <- AverageExpression(human_data,
                                   features = gene,
                                   group.by = 'celltype',
                                   slot = 'data') 
gene_cell_exp <- as.data.frame(gene_cell_exp$RNA)

#complexheatmap作图
library(ComplexHeatmap)
#顶部细胞类型注释
df <- data.frame(colnames(gene_cell_exp))
colnames(df) <- 'class'
top_anno = HeatmapAnnotation(df = df,#细胞名/cluster
                             border = T,
                             show_annotation_name = F,
                             gp = gpar(col = 'black'),
                             col = list(class = c('Macrophage'="#9ECABE",
                                                     'T cell'="#F6F5B4",
                                                     'mDC'="#2F528F",
                                                     "Neutrophil"="#E3AD68",
                                                     "Mast"="#ACD45E")))#颜色设置
#数据标准化缩放一下
marker_exp <- t(scale(t(gene_cell_exp),scale = T,center = T))
Heatmap(marker_exp,
        cluster_rows = F,
        cluster_columns = F,
        show_column_names = F,
        show_row_names = T,
        column_title = NULL,
        heatmap_legend_param = list(
          title=' '),
        col = colorRampPalette(c("#0000EF","black","#FDFE00"))(100),
        border = 'black',
        rect_gp = gpar(col = "black", lwd = 1),
        row_names_gp = gpar(fontsize = 10),
        column_names_gp = gpar(fontsize = 10),
        top_annotation = top_anno)

图片

重点知识来了，为热图行名添加分屏注释：

col_cluster <- setNames(c(rep("#9ECABE",5), rep("#F6F5B4",6),
                          rep("#2F528F",5), rep("#E3AD68",5),
                          rep("#ACD45E",4)),
                        rownames(marker_exp))#设置对应标签颜色

row_info = rowAnnotation(foo = anno_text(rownames(marker_exp), 
                              location = 0, 
                              just = "left",
                              gp = gpar(fill = col_cluster, 
                                        col = "black"),
                              width = max_text_width(rownames(marker_exp))*1.2))


Heatmap(marker_exp,
        cluster_rows = F,
        cluster_columns = F,
        show_column_names = F,
        show_row_names = T,
        column_title = NULL,
        heatmap_legend_param = list(
          title=' '),
        col = colorRampPalette(c("#0000EF","black","#FDFE00"))(100),
        border = 'black',
        rect_gp = gpar(col = "black", lwd = 1),
        row_names_gp = gpar(fontsize = 10),
        column_names_gp = gpar(fontsize = 10),
        top_annotation = top_anno)+row_info```

图片

legend自己修饰一下就可以了。Complexheatmap真的很强大，有很多有用的功能，慢慢的我们探索。觉得分享有用的、点个赞、分享下再走呗！